Long‐term pedogenesis leads to important changes in the availability of soil nutrients, especially nitrogen (N) and phosphorus (P). Changes in the availability of micronutrients can also occur, but ...are less well understood. We explored whether changes in leaf nutrient concentrations and resorption were consistent with a shift from N to P limitation of plant productivity with soil age along a > 2‐million‐year dune chronosequence in south‐western Australia. We also compared these traits among plants of contrasting nutrient‐acquisition strategies, focusing on N, P and micronutrients. The range in leaf P for individual species along the chronosequence was exceptionally large for both green (103–3000 μg P g⁻¹) and senesced (19–5600 μg P g⁻¹) leaves, almost equalling that found globally. From the youngest to the oldest soil, cover‐weighted mean leaf P declined from 1840 to 228 μg P g⁻¹, while P‐resorption efficiency increased from 0% to 79%. All species converged towards a highly conservative P‐use strategy on the oldest soils. Declines in cover‐weighted mean leaf N with soil age were less strong than for leaf P, ranging from 13.4 mg N g⁻¹ on the youngest soil to 9.5 mg N g⁻¹ on the oldest soil. However, mean leaf N‐resorption efficiency was greatest (45%) on the youngest, N‐poor soils. Leaf N:P ratio increased from 8 on the youngest soil to 42 on the oldest soil. Leaf zinc (Zn) concentrations were low across all chronosequence stages, but mean Zn‐resorption efficiency was greatest (55–74%) on the youngest calcareous dunes, reflecting low Zn availability at high pH. N₂‐fixing species had high leaf N compared with other species. Non‐mycorrhizal species had very low leaf P and accumulated Mn across all soils. We surmise that this reflects Mn solubilization by organic acids released for P acquisition. Synthesis. Our results show community‐wide variation in leaf nutrient concentrations and resorption that is consistent with a shift from N to P limitation during long‐term ecosystem development. High Zn resorption on young calcareous dunes supports the possibility of micronutrient co‐limitation. High leaf Mn on older dunes suggests the importance of carboxylate release for P acquisition. Our results show a strong effect of soil nutrient availability on nutrient‐use efficiency and reveal considerable differences among plants of contrasting nutrient‐acquisition strategies.
We study metal absorption around 854 z ≈ 2.4 star-forming galaxies taken from the Keck Baryonic Structure Survey. The galaxies examined in this work lie in the fields of 15 hyperluminous background ...quasi-stellar objects, with galaxy impact parameters ranging from 35 proper kpc (pkpc) to 2 proper Mpc (pMpc). Using the pixel optical depth technique, we present the first galaxy-centred 2D maps of the median absorption by O vi, N v, C iv, C iii, and Si iv, as well as updated results for H i. At small galactocentric radii we detect a strong enhancement of the absorption relative to randomly located regions that extend out to at least 180 pkpc in the transverse direction, and ±240 km s−1 along the line of sight (LOS, ∼1 pMpc in the case of pure Hubble flow) for all ions except N v. For C iv (and H i) we detect a significant enhancement of the absorption signal out to 2 pMpc in the transverse direction, corresponding to the maximum impact parameter in our sample. After normalizing the median absorption profiles to account for variations in line strengths and detection limits, in the transverse direction we find no evidence for a sharp drop-off in metals distinct from that of H i. We argue instead that non-detection of some metal-line species in the extended circumgalactic medium is consistent with differences in the detection sensitivity. Along the LOS, the normalized profiles reveal that the enhancement in the absorption is more extended for O vi, C iv, and Si iv than for H i. We also present measurements of the scatter in the pixel optical depths, covering fractions, and equivalent widths as a function of projected galaxy distance. Limiting the sample to the 340 galaxies with redshifts measured from nebular emission lines does not decrease the extent of the enhancement along the LOS compared to that in the transverse direction. This rules out redshift errors as the source of the observed redshift-space anisotropy and thus implies that we have detected the signature of gas peculiar velocities from infall, outflows, or virial motions for H i, O vi, C iv, C iii, and Si iv.
Ultra-slow, ∼0.1-Hz variations in the oxygenation level of brain blood are widely used as an fMRI-based surrogate of “resting-state” neuronal activity. The temporal correlations among these ...fluctuations across the brain are interpreted as “functional connections” for maps and neurological diagnostics. Ultra-slow variations in oxygenation follow a cascade. First, they closely track changes in arteriole diameter. Second, interpretable functional connections arise when the ultra-slow changes in amplitude of γ-band neuronal oscillations, which are shared across even far-flung but synaptically connected brain regions, entrain the ∼0.1-Hz vasomotor oscillation in diameter of local arterioles. Significant confounds to estimates of functional connectivity arise from residual vasomotor activity as well as arteriole dynamics driven by self-generated movements and subcortical common modulatory inputs. Last, methodological limitations of fMRI can lead to spurious functional connections. The neuronal generator of ultra-slow variations in γ-band amplitude, including that associated with self-generated movements, remains an open issue.
Drew et al. review the linkage of two ultra-slow rhythms in brains: broadband ∼0.1-Hz oscillations in the diameter of arterioles and, similarly, broadband modulation of γ-oscillations in neuronal activity. The linkage underlies “functional connectivity” deduced from BOLD fMRI.
Soil chronosequences provide valuable model systems to investigate pedogenesis and associated effects of nutrient availability on biological communities. However, long-term chronosequences occurring ...under seasonally dry climates remain scarce. We assessed soil development and nutrient dynamics along the Jurien Bay chronosequence, a 2 million-year sequence of coastal dunes in southwestern Australia. The chronosequence is significant because it occurs in a Mediterranean climate and supports hyperdiverse shrublands within a global biodiversity hotspot. Young soils formed during the Holocene (<6,500 years old) are strongly alkaline and contain abundant carbonate, which is leached from the profile within a few thousand years. Middle Pleistocene soils (ca 120,000–500,000 years old) are yellow decalcified sands with residual iron oxide coatings on quartz grains over a petrocalcic horizon that occurs at increasing depth as soils age. Early Pleistocene soils (>2,000,000 years old) are completely leached of iron oxides and consist of bleached quartz sand several meters deep. Changes in soil organic matter and nutrient status along the Jurien Bay chronosequence are consistent with patterns observed along other long-term chronosequences and correspond closely to expectations of the Walker and Syers (1976) model of biogeochemical change during pedogenesis. Organic carbon and nitrogen (N) accumulate rapidly to maximum amounts in intermediate-aged Holocene dunes and then decline as soils age. In contrast, total phosphorus (P) declines continuously along the chronosequence to extremely low levels after 2 million years of pedogenesis, eventually representing some of the lowest P soils globally. Ratios of soil organic carbon to P and N to P increase continuously along the chronosequence, consistent with a shift from N limitation on young soils to extreme P limitation on old soils. Phosphorus fractionation by sequential extraction reveals a rapid decline in primary and non-occluded phosphate and an increase in organic and occluded P as soils age. Concentrations of extractable (that is, readily bioavailable) N and P, as well as exchangeable cations, are greatest in Holocene dunes and decline to low levels in Pleistocene dunes. Extractable micronutrient concentrations were generally very low and varied little across the chronosequence. We conclude that the Jurien Bay chronosequence is an important example of changing patterns of nutrient limitation linked to long-term soil and ecosystem development under a Mediterranean climate.
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•PLS-DA, PC-DFA, SVM and RF analyses were compared for metabolomics analyses.•Parsimonious models for feature selection and data reduction were presented.•Comparisons include ...generally recognized pros along with specific caveats for each of the methods.•Statistical models applied in the analysis of metabolomics data were shown.•Pros and cons of common analytical techniques used in metabolomics studies are highlighted.
The predominance of partial least squares-discriminant analysis (PLS-DA) used to analyze metabolomics datasets (indeed, it is the most well-known tool to perform classification and regression in metabolomics), can be said to have led to the point that not all researchers are fully aware of alternative multivariate classification algorithms. This may in part be due to the widespread availability of PLS-DA in most of the well-known statistical software packages, where its implementation is very easy if the default settings are used. In addition, one of the perceived advantages of PLS-DA is that it has the ability to analyze highly collinear and noisy data. Furthermore, the calibration model is known to provide a variety of useful statistics, such as prediction accuracy as well as scores and loadings plots. However, this method may provide misleading results, largely due to a lack of suitable statistical validation, when used by non-experts who are not aware of its potential limitations when used in conjunction with metabolomics. This tutorial review aims to provide an introductory overview to several straightforward statistical methods such as principal component-discriminant function analysis (PC-DFA), support vector machines (SVM) and random forests (RF), which could very easily be used either to augment PLS or as alternative supervised learning methods to PLS-DA. These methods can be said to be particularly appropriate for the analysis of large, highly-complex data sets which are common output(s) in metabolomics studies where the numbers of variables often far exceed the number of samples. In addition, these alternative techniques may be useful tools for generating parsimonious models through feature selection and data reduction, as well as providing more propitious results. We sincerely hope that the general reader is left with little doubt that there are several promising and readily available alternatives to PLS-DA, to analyze large and highly complex data sets.
Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As ...in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines.
Magnetic reconnection is a fundamental physical process in plasmas whereby stored magnetic energy is converted into heat and kinetic energy of charged particles. Reconnection occurs in many ...astrophysical plasma environments and in laboratory plasmas. Using measurements with very high time resolution, NASA's Magnetospheric Multiscale (MMS) mission has found direct evidence for electron demagnetization and acceleration at sites along the sunward boundary of Earth's magnetosphere where the interplanetary magnetic field reconnects with the terrestrial magnetic field. We have (i) observed the conversion of magnetic energy to particle energy; (ii) measured the electric field and current, which together cause the dissipation of magnetic energy; and (iii) identified the electron population that carries the current as a result of demagnetization and acceleration within the reconnection diffusion/dissipation region.
Soil biota influence plant performance through plant-soil feedback, but it is unclear whether the strength of such feedback depends on plant traits and whether plant-soil feedback drives local plant ...diversity. We grew 16 co-occurring plant species with contrasting nutrient-acquisition strategies from hyperdiverse Australian shrublands and exposed them to soil biota from under their own or other plant species. Plant responses to soil biota varied according to their nutrient-acquisition strategy, including positive feedback for ectomycorrhizal plants and negative feedback for nitrogen-fixing and nonmycorrhizal plants. Simulations revealed that such strategy-dependent feedback is sufficient to maintain the high taxonomic and functional diversity characterizing these Mediterranean-climate shrublands. Our study identifies nutrient-acquisition strategy as a key trait explaining how different plant responses to soil biota promote local plant diversity.
Energetic particle injections are critical for supplying particles and energy to the inner magnetosphere. Recent case studies have demonstrated a good correlation between injections and transient, ...narrow, fast flow channels as well as earthward reconnection (dipolarization) fronts in the magnetotail, but statistical observations beyond geosynchronous orbit (GEO) to verify the findings were lacking. By surveying trans‐geosynchronous injections using Time History of Events and Macroscale Interactions during Substorms (THEMIS), we show that their likely origin is the earthward traveling, dipolarizing flux bundles following near‐Earth reconnection. The good correlation between injections and fast flows, reconnection fronts and impulsive, dawn‐dusk electric field increases is not limited to within 12 RE but extends out to 30 RE. Like near‐Earth reconnection, both ion and electron injections are most probable in the premidnight sector. Similar to bursty bulk flows (BBFs), injection‐time flow speeds are faster farther from Earth. With faster flows, injection intensity generally increases and extends to higher energy channels. With increased geomagnetic activity, injection occurrence rate increases (akin to that of BBFs) and spectral hardening occurs (κ decreases). The occurrence rate increase within the inner magnetosphere suggests that injections populate the radiation belts more effectively under enhanced activity. Our results are inconsistent with the classical concept of an azimuthally wide injection boundary moving earthward from ~9 to 12 RE to GEO under an enhanced cross‐tail electric field. Rather, particle injection and transport occur along a large range of radial distances due to effects from earthward penetrating, azimuthally localized, transient, strong electric fields of recently reconnected, dipolarizing flux bundles.
Key Points
Injections are correlated to reconnection‐related phenomena like fast flows
Injection occurrence rates increase with geomagnetic activity
Injection occurrence rate has dawn‐dusk asymmetry preferring premidnight
Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 as a highly transmissible pathogenic human betacoronavirus. The viral spike glycoprotein (S) utilizes angiotensin-converting ...enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. As SARS-CoV enters host cells, the viral S is believed to undergo a number of conformational transitions as it is cleaved by host proteases and binds to host receptors. We recently developed stabilizing mutations for coronavirus spikes that prevent the transition from the pre-fusion to post-fusion states. Here, we present cryo-EM analyses of a stabilized trimeric SARS-CoV S, as well as the trypsin-cleaved, stabilized S, and its interactions with ACE2. Neither binding to ACE2 nor cleavage by trypsin at the S1/S2 cleavage site impart large conformational changes within stabilized SARS-CoV S or expose the secondary cleavage site, S2'.
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